New Jersey Sen. Robert Menendez has written a personal check of $58,000 to reimburse a donor for two round-trip flights he took on a private jet to the Dominican Republic.

Menendez's office said Thursday the three-year delay in paying for the plane trips with fundraiser and friend Dr. Salomen Melgen was an “oversight.”

“This was sloppy,” Dan O’Brien, Menendez’ chief of staff, told NBC News about the senator's failure to pay for the 2010 flights at the time. “I’m chalking it up to an oversight.”

Several Republicans have accused Melgen, a West Palm Beach eye doctor, of improperly providing Menendez with free flights on his private jet as well as stays at his luxury villa in the Casa de Campo resort.

Asked whether the senator has been contacted by the Senate Ethics Committee about the matter, O’Brien said, “We can assume the Senate Ethics Committee is looking at the allegation.”

News of the senator paying for two private plane trips to the Dominican Republic comes after FBI agents and investigators from the Department of Health and Human Services Office of Inspector General searched the doctor's Florida offices this week. Officials would not comment on the investigation.

In a statement early Wednesday, Menendez said Melgen has been a friend for years and that he had made all appropriate payments, and that he "traveled on Dr. Melgen's plane on three occasions, all of which were paid for and reported appropriately. Any allegations of engaging in prostitutes are manufactured by a politically-motivated right-wing blog and are false."

Those allegations refer to The Daily Caller's unconfirmed report last year, and an ethics complaint from Republicans, that Melgen helped procure prostitutes for Menendez in the Dominican Republic.

New Jersey Republicans filed an ethics complaint against Menendez in November, alleging he accepted free flights to the Dominican Republic and stays at Casa de Campo from the doctor, in violation of Senate rules.

Writing to the Senate Ethics Committee, the Republican ethics complaint alleged Menendez flew on "a private jet to the Dominican Republic and and other locations ... soliciting prostitution."

Last July, the non-partisan Citizens for Responsibility and Ethics in Washington (CREW) received unsubstantiated allegations about Menendez from a mystery man named "Peter Williams" and forwarded the allegations to the FBI, which sources say opened a preliminary investigation. The head of the group is expressing doubts about the information they had received.

“On July 17, 2012, taking the allegations made by 'Pete Williams' against Sen. Menendez quite seriously, CREW forwarded the information to the FBI and the Criminal Division of the Department of Justice," the statement read. "Nevertheless, Mr. Williams’ repeated refusals to agree to telephone or in-person interviews – combined with the concerted efforts of Republican political operatives to market the story – suggest that the whole thing may just be a set-up.”

Weysan Dun, a former director of the New Jersey FBI office, said the Justice Department would have to investigate allegations raised about possible criminal conduct involving a public official.

“The FBI certainly does not want to do anything that would unfairly impugn the reputation of someone, particularly if the allegations are unfounded,” Dun said. “So these are among the most difficult cases to work. You have to be aggressive and thorough, but you also have to be discreet and careful.”

Melgen is a major Democratic political donor and fundraiser who together with family has contributed more than $200,000 to Democratic candidates, including $33,000 to Menendez.

A spokesman for Melgen said in a statement that "the government has not informed Dr. Melgen what concerns it may have."

"We are confident that Dr. Melgen has acted appropriately at all times," said Dean Willbur Jr.

O’Brien provided to NBC News new details about Menendez’ relationship with the Florida doctor. He said Menendez and the doctor have been longtime personal friends and that the senator has visited Melgen at his home in the Dominican Republican “about twice a year," including attending Melgen’s daughter’s wedding. He said Menendez has generally flown commercial for those flights and paid for them out of his own pocket.

But he confirmed that Melgen has also been an active fundraiser for Menendez, holding events for him at his home in South Florida as well as at the Dominican resort.

The senator took three flights aboard Melgen’s jet in 2010; one in May involved travel to Puerto Rico and the Dominican Republican for political fundraisers, O’Brien said. One of those fundraisers was at Melgen’s home in the Dominican Republic, O’Brien said. The May 2010 flights for fundraisers on the two islands were paid for at the time by the Democratic Senatorial Campaign Committee, which Menendez then chaired.

But after reviewing Menendez’ schedule following the ethics complaint late last year, his aides found that the senator had taken two additional flights aboard Melgen’s corporate jet. One was in August 2010 from south Florida to the Dominican Republic and back to south Florida. Another in September was from Teterboro Airport in New Jersey to the Dominican Republican and back to New Jersey. In at least one of those flights, Menendez brought along guests, O’Brien said.

O’Brien said that after the review, spurred by the ethics complaint, Menendez wrote the $58,500 check to Melgen’s company from his personal account. Under Senate ethics rules, senators are allowed to accept gifts from personal friends, but any valued at more than $250 must be publicly reported and approved by the Senate Ethics Committee.